sct_dmri_moco - cropped vs non-cropped image

[valosekj]

I'm wondering about the following thing:

• on line 275, the DWI image is cropped (the output is "${file_dwi}"_crop.nii.gz)
• but then, on line 277, motion correction is done on the original, non-cropped image (${file_dwi}.nii.gz)

spine-park/batch_processing.sh

Lines 274 to 277 in e3cc60a

	# Crop data for faster processing
	sct_crop_image -i "${file_dwi}".nii.gz -m "${file_dwi_seg}".nii.gz -dilate 15x15x0 -o "${file_dwi}"_crop.nii.gz
	# Motion correction
	sct_dmri_moco -i ${file_dwi}.nii.gz -bvec ${file_bvec} -x spline

Isn't file_dwi="${file_dwi}_crop" missing between lines 275 and 277?

[jcohenadad]

Amazing. Good catch @valosekj and thank you for reporting it!!

[jcohenadad]

I fixed the issue in 84ba26f, can you make sure it works fine @Kaonashi22 and if so we can close the issue

[Kaonashi22]

I'm re-running, I'll let you know how it works!